Abstract
Plus-strand RNA viruses contain RNA elements within their genomes that mediate a variety of fundamental viral processes. The traditional view of these elements is that of local RNA structures. This perspective, however, is changing due to increasing discoveries of functional viral RNA elements that are formed by long-range RNA–RNA interactions, often spanning thousands of nucleotides. The plus-strand RNA genomes of tombusviruses exemplify this concept by possessing different long-range RNA–RNA interactions that regulate both viral translation and transcription. Here we report that a third fundamental tombusvirus process, viral genome replication, requires a long-range RNA–based interaction spanning ∼3000 nts. In vivo and in vitro analyses suggest that the discontinuous RNA platform formed by the interaction facilitates efficient assembly of the viral RNA replicase. This finding has allowed us to build an integrated model for the role of global RNA structure in regulating the reproduction of a eukaryotic RNA virus, and the insights gained have extended our understanding of the multifunctional nature of viral RNA genomes.
Highlights
Plus-strand RNA viruses infect a wide variety of organisms and are responsible for causing significant diseases in plants, animals, and humans
These RNA genomes are multifunctional molecules that possess regulatory mechanisms to ensure that these different processes occur accurately and at the proper time during the infectious cycle. Integral to this control is the presence of different regulatory RNA elements within viral genomes that act as signals for modulating molecular events. Such RNA elements have been viewed as localized sequences or structures (e.g. RNA hairpins); this perspective is rapidly changing due to increasing discoveries of functional viral RNA elements that are formed by long-range RNA–RNA interactions spanning significant distances [4,5,6,7,8,9]
It should be noted that the upstream linker (UL)–downstream linker (DL) interaction is not a direct interaction between region II (RII) and RIV; instead, it could function as an RNA–based bridge that juxtaposes the two RNA elements
Summary
Plus-strand RNA viruses infect a wide variety of organisms and are responsible for causing significant diseases in plants, animals, and humans. Besides being templates for replication, plus-strand RNA genomes serve additional functions during infections, including acting as templates for (i) translation of viral proteins, (ii) transcription of viral mRNAs, and (iii) assembly of virus particles. These RNA genomes are multifunctional molecules that possess regulatory mechanisms to ensure that these different processes occur accurately and at the proper time during the infectious cycle. Integral to this control is the presence of different regulatory RNA elements within viral genomes that act as signals for modulating molecular events. Our structural concept of a functional viral RNA genome is shifting from that of a ‘‘linear’’ molecule to one that is three-dimensional [4]
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